Now that people can get Monsters as mercenaries, given the limit of 3 being able to be active at once, I think you should be able to re-order your mercenaries like you can Youkai, so you can actually select which ones will be used. (right now the game only uses the three mercenaries at the top of your list).

Or, alternatively, raise the limit (on a per person basis). To say, maybe 5 per person. Or if it's actually changed to a per person basis, 3 might just be fine anyways, but as it stands, it's three for the entire party (given this used to be a non-issue since there were only three unique mercenaries anyways).